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Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes

Part of the Methods in Molecular Biology book series (MIMB,volume 2148)

Abstract

Efficient and consistent chromosome identification is the foundation for successful cytogenetic studies. Fluorescent in situ hybridization (FISH) has been the most popular technique for chromosome identification in plants. Large insert genomic DNA clones, such as bacterial artificial chromosome (BAC) clones, and repetitive DNA sequences have been the most commonly used DNA probes for FISH. However, most of such traditional probes can only be used to identify a single chromosome or are too polymorphic to consistently identify the same chromosome in the target species. In contrast, FISH using oligonucleotide (oligo)-based probes is highly versatile. In this procedure, a large number of oligos specific to a chromosomal region, to an entire chromosome, or to multiple chromosomes are computationally identified, synthesized in parallel, and labeled as probes. In addition, each oligo probe can be used for thousands of FISH experiments and represents an infinite resource. In this chapter we describe a detailed protocol for amplification and labeling of oligo-based probes, relevant chromosome preparation, and FISH procedures.

Key words

  • Chromosome identification
  • Chromosome painting
  • FISH
  • Oligo-FISH
  • Oligonucleotide probes

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References

  1. Jiang JM, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068

    CAS  CrossRef  Google Scholar 

  2. McClintock B (1929) Chromosome morphology in Zea mays. Science 69:629

    CAS  CrossRef  Google Scholar 

  3. Jiang JM, Gill BS, Wang GL et al (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci U S A 92(10):4487–4491

    CAS  CrossRef  Google Scholar 

  4. Lysak MA, Fransz PF, Ali HBM et al (2001) Chromosome painting in Arabidopsis thaliana. Plant J 28:689–697

    CAS  CrossRef  Google Scholar 

  5. Mukai Y, Yumiko N, Maki Y (1993) Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome 36:489–494

    CAS  CrossRef  Google Scholar 

  6. Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A 101:13554–13559

    CAS  CrossRef  Google Scholar 

  7. Lamb JC, Danilova T, Bauer MJ et al (2007) Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 175:1047–1058

    CAS  CrossRef  Google Scholar 

  8. Danilova TV, Friebe B, Gill BS (2012) Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 121(6):597–611

    CAS  CrossRef  Google Scholar 

  9. Beliveau BJ, Joyce EF, Apostolopoulos N et al (2012) Versatile design and synthesis platform for visualizing genomes with oligopaint FISH probes. Proc Natl Acad Sci U S A 109:21301–21306

    CAS  CrossRef  Google Scholar 

  10. Han YH, Zhang T, Thammapichai P et al (2015) Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 200:771–779

    CrossRef  Google Scholar 

  11. Jiang JM (2019) Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res 27. https://doi.org/10.1007/s10577-019-09607-z

  12. Braz GT, He L, Zhao H et al (2018) Comparative Oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 208:513–523

    CAS  CrossRef  Google Scholar 

  13. He L, Braz GT, Torres GA et al (2018) Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 127:505–513

    CrossRef  Google Scholar 

  14. Qu MM, Li K, Han Y et al (2017) Integrated karyotyping of woodland strawberry (Fragaria vesca) with oligopaint FISH probes. Cytogenet Genome Res 153:158–164

    CrossRef  Google Scholar 

  15. Hou LL, Xu M, Zhang T et al (2018) Chromosome painting and its applications in cultivated and wild rice. BMC Plant Biol 18:110

    CrossRef  Google Scholar 

  16. Meng Z, Zhang Z, Yan T et al (2018) Comprehensively characterizing the cytological features of Saccharum spontaneum by the development of a complete set of chromosome-specific oligo probes. Front Plant Sci 9:1624

    CrossRef  Google Scholar 

  17. Albert PS, Zhang T, Semrau K et al (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc Natl Acad Sci U S A 116:1679–1685

    CAS  CrossRef  Google Scholar 

  18. Murgha YE, Rouillard J-M, Gulari E (2014) Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries. PLoS One 9:e94752

    CrossRef  Google Scholar 

  19. De Carvalho CR, Saraiva LS (1993) An Air Drying Technique for Maize Chromosomes without Enzymatic Maceration. Biotech Histochem 68:142–145

    Google Scholar 

  20. Schubert I, Fransz PF, Fuchs J, de Jong JH (2001) Chromosome painting in plants. Methods Cell Sci 23:57–69

    Google Scholar 

  21. Ross KJ, Fransz P, Jones GH (1996) A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosom Res 4:507–516

    Google Scholar 

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Acknowledgments

This work was supported by National Science Foundation (NSF) grants MCB-1412948 and IOS-1444514 to J.J.

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Correspondence to Jiming Jiang .

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Braz, G.T., Yu, F., do Vale Martins, L., Jiang, J. (2020). Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes. In: Nielsen, B.S., Jones, J. (eds) In Situ Hybridization Protocols . Methods in Molecular Biology, vol 2148. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0623-0_4

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  • DOI: https://doi.org/10.1007/978-1-0716-0623-0_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0622-3

  • Online ISBN: 978-1-0716-0623-0

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